Novakon Spindle RPM Issue

We recently purchased a Novakon NM-200 Series 2 CNC Mill running Mach 3. The mill ran perfectly for about one month, then last week I was making a small fixture using MDI, I drilled one .250" hole in some 6061-T6 and moved to the next hole, typed S1200 M03 and hit enter, the spindle raced up to a very high rpm (something over 6000rpm) and then stopped working. We then started inspecting the machine for damage and noticed the VFD blew off 3 capacitors.
Since the machine is only 6 weeks old and still under warranty Novakon sent us a new VFD, We then installed it and ran the Spindle Calibration program and saved the new curve. Now when you turn on the spindle in MDI, S500 M03, The spindle races up to a high but unknown RPM, my Machinist ears tell me it is around 6000 rpm or so but the Machine states 500RPM. During the spindle calibration the spindle responded perfectly all the way to it's 6000rpm max.

What could be the issue? Any help will be greatfully appreciated.

Thanks
Brent